Download Model 02_Antibiotics

Biology 260
Model Building Exercise 02
Stage 03 – Antimicrobials: Susceptibility & Resistance
Building a model to explain a natural phenomenon
Natural Phenomenon: Antimicrobial drug resistance is an enormous global health problem. Many bacteria
and viruses were once susceptible to many different antimicrobials, but now they are becoming resistant. How
does antimicrobial drug resistance happen??
For this unit you will be responsible for writing up your own individual model that explains the BIG PICTURE
of how a population of bacteria or viruses can become resistant to antimicrobial drugs. You’ll want to study
your reading guides to get more of the details. This model is designed to help you to put all of the concepts that
we have been studying together in two side-by-side stories, one for bacteria and one for viruses, and to help you
to study for the exam. The next few paragraphs will answer the following questions:
1) How will I organize my model?
2) What is the format?
3) Checklist of terms and concepts to have in your model
1) How will I organize my model?
This model will tell the side-by-side stories of how a population of bacteria and a population of viruses can, at
first, be susceptible to an antimicrobial drug and how they can then become resistant to it. Here is how I
suggest you organize your story:
BACTERIA: ANTIMICROBIAL SUSCEPTIBILITY AND RESISTANCE
Our back story: Now that a pathogenic bacterium has been transmitted to our patient by getting past our
microbial control methods, has made it past the patient’s normal microbiota, has found the right environment
and nutrients, has harvested energy, and has grown through binary fission, we’ve gone from one bacterium to a
population of millions of bacteria now causing disease.
1. This population of bacteria, through quorum sensing, can build a biofilm as protection from the
environment (including antimicrobial drugs, microbial control methods, and the immune system).
2. Each bacterium in that population, through gene regulation, can respond to its environment to efficiently
obtain and utilize nutrients.
3. The population of pathogenic bacteria is now causing disease, so our patient is given an antimicrobial.
How can a population of bacteria be susceptible?
a. Most antimicrobials work to inhibit enzymes or molecules (targets) that function during cell
growth:
i. Cell wall synthesis
ii. Protein synthesis
iii. Nucleic acid synthesis
iv. Folate biosynthesis
b. Many of these antimicrobials work through competitive or noncompetitive inhibition of the
specific enzyme or molecule (a target) that is required for these synthesis pathways.
c. Each antimicrobial must
i. Exhibit selective toxicity
ii. Have access to its target
4. However, over time, that population of bacteria, once susceptible to the antimicrobial, is now resistant.
a. How can a bacterium resist an antimicrobial drug? Resistance traits!!
i. Drug-inactivating enzymes
ii. Increased elimination
iii. Decreased uptake
iv. Alteration in target molecule
b. How can a population of bacteria become resistant? Natural Selection!
i. Resistance traits are pre-existing variations in a population
1. Random mutations during DNA replication
2. Horizontal gene transfer
a. Transformation
b. Transduction
c. Conjugation
ii. Selection by the antimicrobial
iii. Genetic inheritance of the resistance trait
ANIMAL VIRUSES: ANTIVIRAL SUSCEPTIBILITY AND RESISTANCE
1. An animal virus infection can result in either
a. a productive infection or
b. a latent state.
2. Viruses infect eukaryotes.
a. How do viruses replicate? HIV, Influenza
b. How do antiviral drugs work?
c. How can a population of viruses become drug-resistant?
i. Natural selection
1. Pre-exisiting resistance trait variations in a population
a. Random mutations during replication
i. Reverse transcriptase (HIV)
ii. Replicase (influenza)
b. Genome reassortment (influenza)
2. Selection by antiviral drug
3. Genetic inheritance of the resistance trait
4. Adaptation
2) What is the format? Like before, the model is designed to be a study-aid for you, so do not feel like you
have to make it in publishable form. You can write it on the computer or whip out some paper and write it by
hand, as long as I can read it, so it must be neat. Create your model using both pictures and words to explain
the concepts and how they interconnect. Draw your model as a picture storybook supplemented with words
on regular paper. All drawings, figures, and diagrams must be hand-drawn or computer-aided and labeled, but
they cannot be electronically copied and pasted.
Below is a checklist of the key words and concepts that MUST be in your model. Just check them off as you
write, draw, and label to make sure that you have included them all. I will be using this checklist to grade your
model. Keep your model to between 3-10 pages. Length is not too important, just be sure to have everything
from the checklist on it and interconnect the concepts in order to tell a story.
3) Checklist of terms and concepts to have in your model.
BACTERIA – ANTIMICROBIAL SUSCEPTIBILITY AND RESISTANCE
1. Building a biofilm through quorum sensing
 Redraw Figure 4.3 (Development of a Biofilm)
 Inbetween steps 1 and 2
o insert Figure 7.18 (Quorum sensing)
o insert Figure 7.19 (Two-Component Regulatory System) which signals the production of the
biofilm.
2. Obtaining nutrients through gene regulation
 Regulating enzyme systems based on nutrient availability.
o Define the following and give an example of each:
 Operon
 Constitutive
 Inducible
 Repressible
 Explain what is going on in Figure 7.24 (Diauxic Growth Curve of E. coli Growing in a Medium
Containing Glucose and Lactose).
o By using the following Figures:
 Figure 7.25 (Glucose and the lac Operon)
 Figure 7.23 (Lactose of the lac Operon)
 Figure 7.22 (Transcriptional Regulation by Activators)
3. How can a population of bacteria be susceptible to antimicrobial drugs?
 Most antimicrobials work to inhibit enzymes or molecules (targets) that function during cell growth:
o Redraw Figure 20.2
 Most antimicrobials work through competitive or noncompetitive inhibition of a specific enzyme or
molecule (a target) required for cell growth
o Figure 6.15
 Competitive inhibition
 Non-competitive inhibition
 Each antimicrobial must exhibit selective toxicity.
o What is selective toxicity?
o Cell wall synthesis inhibitors
 Redraw Figure 20.3
 What are the target molecules for
• The beta-lactams?
• Vancomycin?
• Bacitracin?
 How do these drugs exhibit selective toxicity?
 How would inhibition of these targets affect cell growth?
o Protein synthesis inhibitors
 Redraw Figure 20.7 (You do not need to know the specific mechanism of each drug. Just
know that each binds to the ribosome (target) to inhibit translation (protein synthesis).
• I know I just told you, but what is the target molecule?
• How do these drugs exhibit selective toxicity?
o prokaryotic ribosome
o eukaryotic ribosome
 How would inhibition of this target affect cell growth?
o Nucleic acid inhibitors
 Draw a Figure to explain how fluoroquinolones work.
• What is the target?
• How do these drugs exhibit selective toxicity?
• How would inhibition of this target affect cell growth?
 Draw a Figure to explain how rifamycins work.
• What is the target?
• How do these drugs exhibit selective toxicity?
• How would inhibition of this target affect cell growth?
 Draw a Figure to explain how metronidazole (Flagyl) works.
• What is the target (what does the drug bind to)?
• How does this drug exhibit selective toxicity?
• How would inhibition of this target affect cell growth?
• What diseases is this drug used to treat?
o Folate biosynthesis inhibitors
 Redraw Figure 20.8(b) (You do not need to know the names of the intermediate
molecules in this Figure. Just know that the drugs inhibit key enzymes in this folate
biosynthesis pathway needed to make nucleotides).
• What are the targets?
• How do these drugs exhibit selective toxicity?
• How would inhibition of this target affect cell growth?
 Each antimicrobial must have access to its target.
o Trace the path of the following antimicrobials
 a cell wall synthesis inhibitor (use filled triangles)
 a protein synthesis inhibitor (use filled circles)
o from the outside of the cell to its target in both
 a Gram-positive cell, and
 a Gram-negative cell
o Make sure to include the following where appropriate:
 Cytoplasmic membrane
 Transport proteins
 Peptidoglycan
 Outer membrane
 Porins
 Biofilm (EPS)
Model 02 continued…
4. However, over time, that population of bacteria, once susceptible to the antimicrobial, is now resistant.
 How can a bacterium resist an antimicrobial drug? Resistance traits!!
o Redraw Figure 20.14 and explain how each trait works to cause drug resistance.
 Drug-inactivating enzymes
 Increased elimination
 Decreased uptake
 Alteration in target molecule
 How can a population of bacteria become resistant? Natural Selection!
o Redraw Figure 20.13 and answer the following questions (from Reading Guide 08):
A) Population Growth: How does the population growth of bacteria change over time?
Draw a graph with time on the x-axis and number of bacteria on the y-axis. The initial timepoint on
our x-axis (let’s call this Time 0) is our population of bacteria before the drug is given (top of Figure
20.13), the next timepoint (Time 1) is our population of bacteria after initial exposure to the
antimicrobial drug (middle of Figure 20.13), and the last timepoint (Time 2) is our population of bacteria
sometime later, but still in the presence of the antimicrobial drug (bottom of Figure 20.13).
B) Variation: Now let’s describe the variation of this population of bacteria in Figure 20.13:
Before the antimicrobial drug is given (top of Figure 20.13), are there any resistant strains already
present in the population? How do you think they came about? Make your initial hypotheses here, then
keep reading in this section to learn more.
C) Pre-Existing Variation: Would you say that the resistant bacteria were pre-existing (already
present) in the population before exposure to the drug, or did the drug cause that one bacterium to
change from being sensitive to being resistant to the drug?
D) Selection: You can see in Figure 20.13 that the resistant bacteria are being selected for by the
drug in their environment. Would you say this is a random (happens by chance) selection or a
nonrandom (happens by a very specific mechanism) selection? Why?
E) Inheritance: Does inheritance of genetic information play a role in the development of drug
resistance? How?
F) Adaptation: What evidence from this Figure could you use to support this statement, “The
bacterial population adapted to the drug” (Hint: How does the population at the bottom of Figure 20.13
differ from the population at the top? What drug environment is the population at the top in, compared
to the population at the bottom?)
G) Natural Selection: To sum this figure up, write a paragraph that explains how drug resistance
happens by natural selection using the following key terms: population, pre-exisiting variation,
selection, inheritance, adaptation
o How do populations get pre-existing variations?? Resistance traits are pre-existing variations
in a population. How do those resistance traits become pre-existing in the first place?
 Random mutations during DNA Replication can make daughter cells with different
DNA sequences (some cells have the new mutation, others don’t)!
• DNA polymerase inserts incorrect base pair, repair mechanisms fail to correct it
• Base substitution
o Silent
o Missense
o Nonsense
• Deletion/Addition of nucleotides
o Frameshift
• Repair mechanisms
o Proofreading by DNA Polymerase
o Mismatch repair

Horizontal gene transfer, where entire genes are transferred from a source to a recipient
cell in a population, can make variations (some cells in the population have the new gene,
others don’t)!!
• Why must transferred DNA be on a replicon in order to be passed to daughter
cells?
• Explain what must happen if the DNA is not on a replicon in order for it to be
passed to daughter cells.
o Homologous recombination
• Copy Table 8.3 on page 201
• DNA-mediated transformation – write a short sentence that describes what it is
o What is a “competent” cell?
o Redraw Figure 8.19 and explain the process
• Transduction – write a short sentence that describes what it is
o Since transduction depends on the life cycle of a bacteriophage, you first
need to understand how bacteriophages (or phages) reproduce.
 Upon infection of a bacterial host cell, bacteriophages can produce
two different states: productive infection and latent state.
• Redraw Figure 13.4
 Lytic cycle: productive infection by a lytic phage
• Redraw Figure 13.5. Draw an arrow from panel 5 back to
panel 1 to infect a new cell – this is the lytic cycle.
 Lysogenic cycle: latent infection by a temperate phage
• Redraw Figure 13.6. Draw an arrow from “Cell Division”
cell back to “Integrated DNA” cell. The prophage is
replicated every time the host cell replicates. This is the
lysogenic cycle.
• Temperate phages reproduce both by lytic infection and
lysogenic infection.
• Lysogenic conversion – what is it? Know two examples
from Table 13.3
o Generalized transduction – transfer of any bacterial genes by lytic phages
 Redraw Figure 8.20
o Specialized transduction – transfer of a few specific bacterial genes by
temperate phages.
 Redraw Figure 13.9
• Conjugation – write a short sentence that describes what it is
o Plasmid Transfer!
 Conjugative plasmids: F plasmids and R plasmids
• What is an F plasmid?
• What is an R plasmid? Redraw Figure 8.25
o Note that each R plasmid must have
 Origin of replication (it is a replicon)
 Origin of transfer
 Pilus-synthesis genes
o Note that each R plasmid can have variable
numbers of different resistance genes
 Figure 8.25 is an example of an R plasmid
with three specific resistance genes on it, but
these are ONLY possibilities of the types of
resistance genes you might find on an R
plasmid.

plasmid transfer mechanism
• Redraw Figure 8.22
 Composite transposons – write a short description of this
• Redraw Figure 8.27 to explain how a formerly
vancomycin-sensitive S. aureus cell can become
vancomycin-resistant.
o Chromosome Transfer!
 Hfr cells and F’ cells
• What are they? Redraw Figure 8.23
 Chromosome transfer mechanism
• Redraw Figure 8.24
VIRUSES – ANTIVIRAL SUSCEPTIBILITY AND RESISTANCE
Since antivirals are often chemicals that directly inhibit an enzyme or protein that is required for completion of
the viral life cycle, let’s start by learning how viruses reproduce.
1. A animal viral infection can result in either
a. a productive infection or
b. a latent state.
c. Figure 13.18
2. Types and structures of animal viruses
a. Naked virus
b. Enveloped virus
i. Figure 13.2
ii. HIV: (Retroviridae) Figure 28.3(a) (don’t worry about 28.3(b))
iii. Influenza: (Orthomyxoviridae) Figure 21.23
c. Genome can be made of
i. DNA or
ii. RNA
3. Animal virus life cycle
a. Attachment
i. HIV: Figure 28.4
ii. Influenza: HA binds to receptor on ciliated host epithelial cells
b. Penetration and uncoating
i. Figure 13.13
ii. NOTE: the book is WRONG about how HIV enters a cell on page 318, but is CORRECT
on page 699. HIV enters a cell by membrane fusion.
iii. NOTE: Influenza enters by endocytosis
c. Synthesis of viral proteins and replication of the genome
i. Don’t worry about Figure 13.14 and the plus- and minus-strands
ii. In order to replicate, viruses need to make
1. more viral genomes (they make their own polymerase for this)
2. more viral proteins (they use host ribosomes for this)
iii. DNA genome?
1. Viral DNA polymerase
a. DNA-dependent DNA polymerase (just like our DNA polymerase)
iv. RNA genome, non-retrovirus? (Influenza)
1. Replicase
a. RNA-dependent RNA polymerase
b. No proofreading ability – makes mistakes
v. RNA genome, retrovirus? (HIV) – Figure 28.5
1. Reverse transcriptase
a. RNA-dependent DNA polymerase
b. No proofreading ability – makes mistakes
2. Integrase
3. Protease
d. Assembly
e. Release
i. Enveloped viruses
1. Figure 13.15
ii. Naked viruses
1. Released when host cell dies (apoptosis – Say “A-poe-toe-sis”)
4. ANTIVIRAL SUSCEPTIBILITY: How do antiviral drugs work?
a. Figure 20.15
i. Entry inhibitors against HIV
ii. Uncoating inhibitors against influenza A
iii. Nucleic Acid synthesis inhibitors against HIV
1. Inhibit reverse transcriptase
iv. Integrase inhibitors against HIV
v. Assembly and release inhibitors
1. Against HIV: Inhibit protease
2. Against Influenza A: Inhibit neuraminidase (NA)
5. ANTIVIRAL RESISTANCE: How does a population of viruses become resistant to a drug?
a. Natural selection
i. Pre-exisiting resistance trait variations in a population
1. Random mutations during replication
a. Reverse transcriptase (HIV)
b. Replicase (influenza)
i. Antigenic drift causes seasonal influenza (Figure 21.24(a))
2. Genome reassortment (influenza)
i. Antigenic shift causes pandemic influenza (Figure 21.24(b))
ii. Selection by antiviral drug
iii. Genetic inheritance of the resistance trait
iv. Adaptation to new drug environment. Resistance!!